GO and KEGG enrichment analysis based on cuffdiff

[Roger Z]

Hi,everyone!I used cufflinks and cuffdiff to detect differentially expressed genes, and I am going to do GO and KEGG pathway enrichment analysis based on the result. The problem is that some genes of cuffdiff output have no corresponding GeneID(they are assembled by cufflinks), which makes it impossible to do GO enrichment analysis. Could you please give me some advice? How can we solve this problem?

Best regards,

[Parharn]

I do DESeq2, have you tried that?
And what is your organism?

[kiwistew]

Option one - do this part of the analysis without the novel transcripts. Just do the ontology analysis with expression data for known transcripts.

Option two - try and assign gene ontologies to the novel transcripts. Then included them in the analysis.

Option two would clearly be a lot more work but might be neccesary if you're working on a poorly annotated organism.

[Roger Z]

Thank you, kiwistew. I have chosen option 2 and I used blast2GO.

[Roger Z]

Thank you,Parharn! Organism is zebrafish and the problem has been solved using cuffdiff.